January 2019

Modelling and exploring airline booking data

Author: Andreas Vroutsis
Posted: 25 Jan 2019 | 13:31

From April–December 2018, Rosa Filgueira and I worked at the Dynamic Forecasting project, as members of the Research Engineering Group of the Alan Turing Institute.

Spark-based genome analysis on Cray-Urika and Cirrus clusters

Author: Rosa Filgueira
Posted: 16 Jan 2019 | 11:06

Analysing genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation.

Typically in a cancer genomics analysis, both a tumour sample and a “normal” sample from the same individual are first sequenced using NGS systems and compared using a series of quality control stages. The first control stage, ‘Sequence Quality Control’ (which is optional), checks sequence quality and performs some trimming. While the second one, ‘Alignment’, involves a number of steps, such as alignment, indexing, and recalibration, to ensure that the alignment files produced are of the highest quality as well as several more to guarantee the variants are called correctly. Both stages compromise a series of intermediately computing and data-intensive steps that very often are handcrafted by researchers and/or analysts.

Fortissimo Marketplace: open for business

Author: Mark Sawyer
Posted: 15 Jan 2019 | 11:52

 

The Fortissimo 2 project ended on 31 December 2018. Together with its predecessor (the plain old 'Fortissimo project') it has helped over 100 SMEs and mid-caps to run experiments that demonstrate the effectiveness of providing HPC services using a business model derived from cloud computing, thereby making it much lower risk for small companies to use HPC. 

Catalyst UK programme brings Arm-based HPC system to EPCC!

Author: Michele Weiland
Posted: 8 Jan 2019 | 15:08

Earlier this year, HPE announced the Catalyst UK programme: a collaboration with Arm, SUSE and three UK universities to deploy one of the largest Arm-based high performance computing (HPC) installations in the world. EPCC was chosen as the site for one of these systems; the other two are the Universities of Bristol and Leicester.

EPCC's system (called 'Fulhame' after pioneering chemist Elizabeth Fulhame) was delivered and installed in early December. This HPE Apollo 70-based system consists of 64 compute nodes with two 32-core Cavium ThunderX2 processors (ie 4096 cores in total), 128GB of memory composed of 16 DDR4 DIMMs, and Mellanox InfiniBand interconnects. It will be made available to both industry and academia, with the aim to build applications that drive economic growth and productivity as outlined in the UK government’s Industrial Strategy.

On the frontline of energy-efficient computing

Author: Paul Clark
Posted: 7 Jan 2019 | 15:14

The Advanced Computing Facility (ACF) on the outskirts of Edinburgh is the high performance computing data centre of EPCC.

Built in the 1970s and operated by EPCC since the turn of the millennium, the ACF site has had significant investment over the years. At present, there are three Computer Rooms, imaginatively called: Computer Room 1 (CR1), Computer Room 2 (CR2), and Computer Room 3 (CR3).